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: Additional file 1 Dataset details
The data file of Ogawa and collaborators (namely OC dataset) comes from experiments on the yeast Saccharomyces cerevisiae. Their work concerned the identification of the components of the system of regulation PHO involved in the acquisition of phosphate ADDIN EN.CITE Ogawa200015415415417Ogawa, N.DeRisi, J.Brown, P. O.Department of Biochemistry, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305-5307, USA.New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysisMol Biol Cell4309-211112Acid Anhydride Hydrolases/metabolismAmino Acid SequenceFungal Proteins/genetics*Gene Expression Profiling*Gene Expression Regulation, Fungal*Genome, FungalModels, BiologicalMutationOligonucleotide Array Sequence AnalysisPolyphosphates/*metabolismProton-Translocating ATPases/physiologySaccharomyces cerevisiae/*genetics/*metabolismSequence HomologyTrans-Activators/genetics*Vacuolar Proton-Translocating ATPasesVacuoles/enzymology/metabolism2000Dec11102525http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11102525 [1]. The initial data file comprised expression measurements for 6013 genes in 8 different experimental conditions (several mutant stocks compared with the wild stock with various phosphate concentrations). In a preliminary step, all the pre-existing missing values were eliminated. Only 230 genes were thus removed (3.8%) preserving 5783 genes in the final dataset. We next selected a subset of 827 genes that represented 1/7th of the whole dataset ADDIN EN.CITE de Brevern200411011011017de Brevern, A. G.Hazout, S.Malpertuy, A.Equipe de Bioinformatique Genomique et Moleculaire (EBGM), INSERM E0346, Universite Denis DIDEROT-Paris 7, case 7113, 2, place Jussieu, 75251 Paris, France. alexandre.debrevern@ebgm.jussieu.frInfluence of microarrays experiments missing values on the stability of gene groups by hierarchical clusteringBMC Bioinformatics1145Cluster AnalysisComputational Biology/statistics & numerical dataDatabases, GeneticGene Expression Profiling/methods/*statistics & numerical dataGene Expression Regulation, Fungal/*geneticsGenes, Fungal/*geneticsOligonucleotide Array Sequence Analysis/methods/*statistics & numericaldataReference ValuesResearch Design/statistics & numerical dataSaccharomyces cerevisiae/genetics2004Aug 2315324460http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15324460 [2]. This subset (namely OS) has the interest to be representative of the different behaviors of the complete dataset, but required less computational time for the replacement of missing values and clustering procedures. The data of Gasch and collaborators also relates to the yeast Saccharomyces cerevisiae ADDIN EN.CITE ADDIN EN.CITE.DATA [3]. It includes 6,153 genes for 178 experiments. As the number of missing values was high; we eliminated all the experimental conditions with more than 80 missing data. It remained 42 conditions. Again, different data files were generated. The first included 5,007 genes and the 10 experiments related to the osmotic shock response of mutant and wild type cell exposed to the H2O2. Only 1/7th of the genes were finally used in the analysis (717 genes with 10 conditions, dataset GH2O2). The second comprised 3,643 genes and 8 experiments related to the thermal shock response (at 37C) for 4 successive times (5, 15, 30 and 60 minutes). With this dataset the influence of the missing data on kinetic experiments could be estimated. A subset of genes was selected (1/7th of the dataset) and corresponded to 523 genes and 8 experiments, namely GHeat dataset. Bohen and collaborators have works on human follicular lymphomas, the goal being to study the effect of the ritumibax on patients ADDIN EN.CITE Bohen200315615615617Bohen, S. P.Troyanskaya, O. G.Alter, O.Warnke, R.Botstein, D.Brown, P. O.Levy, R.Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA.Variation in gene expression patterns in follicular lymphoma and the response to rituximabProc Natl Acad Sci U S A1926-301004AdultAgedAntibodies, Monoclonal/*therapeutic useAntineoplastic Agents/*therapeutic useFemale*Gene Expression ProfilingHumansLymphoma, Follicular/*drug therapy/geneticsMaleMiddle AgedTreatment Outcome2003Feb 1812571354http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12571354 [4]. This matrix contained 16,523 genes with 16 experiments where the treatments of the patients were different. In the analysis, we used a subset corresponding to 1/7th of the data, i.e. 861 genes, namely B dataset. A final set came from an experiment carried out by Lucau-Danila and collaborators. The study is related to the determination of the effect of Benomyl stress-induced on Saccharomyces cerevisiae cells, according to time ADDIN EN.CITE Lucau-Danila200515715715717Lucau-Danila, A.Lelandais, G.Kozovska, Z.Tanty, V.Delaveau, T.Devaux, F.Jacq, C.Laboratoire de Genetique Moleculaire, CNRS UMR 8541, Ecole Normale Superieure, 46 rue d'Ulm, 75230 Paris cedex 05, France.Early expression of yeast genes affected by chemical stressMol Cell Biol1860-8255Benomyl/*pharmacologyDNA-Binding Proteins/genetics/*physiologyDown-Regulation/physiologyGene Expression ProfilingGene Expression Regulation, Fungal/*drug effectsGenome, FungalOligonucleotide Array Sequence AnalysisSaccharomyces cerevisiae/drug effects/*geneticsSaccharomyces cerevisiae Proteins/genetics/*physiologySequence Deletion/geneticsStimulation, ChemicalTrans-Activators/genetics/*physiologyTranscription Factors/genetics/*physiologyUp-Regulation/physiology2005Mar15713640http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15713640 [5]. The expression matrix contains 5261 genes and six points of kinetics (30 seconds, 2, 4, 10, 20 and 40 minutes), namely L dataset. The elimination of genes with missing values (11.4 %) reduced the dataset to 4645 genes and 6 experiments.
ADDIN EN.REFLIST 1. Ogawa N, DeRisi J, Brown PO: New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis. Mol Biol Cell 2000, 11(12):4309-4321.
2. de Brevern AG, Hazout S, Malpertuy A: Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering. BMC Bioinformatics 2004, 5:114.
3. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO: Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 2000, 11(12):4241-4257.
4. Bohen SP, Troyanskaya OG, Alter O, Warnke R, Botstein D, Brown PO, Levy R: Variation in gene expression patterns in follicular lymphoma and the response to rituximab. Proc Natl Acad Sci U S A 2003, 100(4):1926-1930.
5. Lucau-Danila A, Lelandais G, Kozovska Z, Tanty V, Delaveau T, Devaux F, Jacq C: Early expression of yeast genes affected by chemical stress. Mol Cell Biol 2005, 25(5):1860-1868.
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